Fix: MCP Server Misinterprets Tool Error Responses

This ticket reports and resolves a bug in the MCP server's tool handling logic that caused it to misinterpret structured error responses from underlying services as schema validation failures.

Problem: When a tool's underlying service (e.g., IssueService.createIssue) returned a structured error object (e.g., {"error": "...", "message": "...", "code": "..."}), the MCP server's CallToolRequestSchema handler incorrectly set the isError flag to false in its response. This led the client (e.g., the Python SDK) to attempt to validate the error object against the tool's success output schema, resulting in a misleading "Structured content does not match the tool's output schema: data should NOT have additional properties" error.

Root Cause: The mcp-stdio.mjs file's CallToolRequestSchema handler unconditionally set isError: false when processing the result from callTool, even if result itself was a structured error object.

Solution: The CallToolRequestSchema handler in mcp-stdio.mjs has been adjusted to correctly identify if the result from callTool is an error object (by checking for the presence of an error property). The isError flag in the MCP server's response is now conditionally set to true if the tool's result is an error, ensuring proper error propagation to the client.

Changes Implemented: The CallToolRequestSchema handler in mcp-stdio.mjs was modified as follows:

        let contentBlock;
        let isServiceError    = false;
        let structuredContent = null;

        if (typeof result === 'object' && result !== null) {
            isServiceError = 'error' in result; // Check for 'error' property to identify service errors

            contentBlock = {
                type: 'text',
                text: JSON.stringify(result, null, 2)
            };
            structuredContent = result;
        } else {
            contentBlock = {
                type: 'text',
                text: String(result)
            };
        }

        const response = {
            content: [contentBlock],
            isError: isServiceError // Set isError based on whether the service result was an error
        };

This ensures that error responses from tools are correctly identified and propagated.